Sequence
atgc intronic sequence ATGC exonic sequenceTGAATGGGAGCTTCTGAATGATGTTAAGGCTATATGGCTGAGAAGTCCAAAGGAGGTGACAGAGGAAGAGTACACTAAATTCTACCACTCTCTCTCAAAGgtgaaaaccatgcgttaactaaatcatacttgttacatactaggtgtaaaattttcgtgtggatttccctgaccccagttgttatacag
Basic information
species | Arabidopsis thaliana |
transcript | AT4G24190.2 |
intron # | 9 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: LOC_Os06g50300.1 (Oryza sativa), 5'ss of exon 9
TGAATGGGAGCTTCTGAATGATGTTAAGGCTATATGGCTGAGAAGTCCAAAGGAGGTGACAGAGGAAGAGTACACTAAATTCTACCACTCTCTCTCAAAGgtgaaaaccatgcgttaactaaatcatacttgttacatactaggtgtaaaattttcgtgtggatttccctgaccccagttgttatacag-----------
||| |||||||||||||||||||| |||||||||||||| | || || |||||||| || || ||||| ||||| || || |||||||| || | ||||| | | ||| | | || | | | | | | | ||||| || | | | | ||| || || ||| |
TGAGTGGGAGCTTCTGAATGATGTGAAGGCTATATGGCTTCGTAGCCCTAAGGAGGTTACTGAAGAAGAATACACAAAGTTTTACCACTCACTTGCTAAGgtacacagactgcagtgatgaatttacaggagcataacattttatgtaagccttgcagaagaaagcaagtaacctcatttaatatcaaattattttgtag
upper sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GRMZM2G141931_T01 (Zea mays), 5'ss of exon 9
TGAATGGGAGCTTCTGAATGATGTTAAGGCTATATGGCTGAGAAGTCCAAAGGAGGTGACAGAGGAAGAGTACACTAAATTCTACCACTCTCTCTCAAAGgtgaaaaccat-gcgttaactaaatca----tacttgttacatact-----aggtgtaaaattttcgtgtggat-ttccctgaccccagttgttatacag--------------------
||| ||||| |||||||||||||| |||||| ||||||| | || ||||||||||| || || ||||| ||| | || || ||||| || || | ||||| || || | || | | | | | |||| | | | | || ||| | ||| | || ||| || |||| |
TGAGTGGGAACTTCTGAATGATGTGAAGGCTGTATGGCTTCGCAGCCCAAAGGAGGTTACCGATGAAGAATACTCGAAGTTTTACCATTCACTAGCCAAGgtaaatactgtagcaatggattagttagtagtactcaacatttgtttttgccaaagaaagctttgcttgtacaccttgtttgataaatatttgtatataacttaacaattcttttttcag
upper sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA17G37820.1 (Glycine max), 5'ss of exon 9
-TGAATGGGAGCTTCTGAATGATGTTAAGGCTATATGGCTGAGAAGTCCAAAGGAGGTGACAGAGGAAGAGTACACTAAATTCTACCACTCTCTCTCAAAGgtgaaaaccatgcgttaactaaatcatacttgttacatactaggtgtaaaattttcgtgtggatttccctgaccccagttgttatacag------------------------------
||||||||| ||| | |||||||| || |||||||||||||| | |||||||||||| ||||| ||||| ||||| ||||||||||||||||| | ||||| | | || | | | | ||| ||| | | | || || | ||| | | | |||| | | |
ATGAATGGGAACTTTTAAATGATGTGAAAGCTATATGGCTGAGGAATCCAAAGGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAggt-agcattgccaatttgccatgct-tgttccttatatatcaaggg--aatttattgtgaaattcacttcactctgagtttgttaatattcataaagttgtggatttatgttttgtgca
upper sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: GLYMA14G40320.2 (Glycine max), 5'ss of exon 9
TGAATGGGAGCTTCTGAATGATGTTAAGGCTATATGGCTGAGAAGTCCAAAGGAGGTGACAGAGGAAGAGTACACTAAATTCTACCACTCTCTCTCAAAGgtgaaaaccatgcgttaactaaatcatacttgttacatactaggtgtaaaattttcgtgtggatttccctgaccccagttgttatacag-------------------------------
||| ||||| ||| | |||||||| || |||||||||||||| | |||||| ||||| ||||| ||||| ||||| ||||||||||||||||| | ||||| | ||| | || | ||| |||||| | || | ||| |||| | ||| || | |||| | | |
TGAGTGGGAACTTTTAAATGATGTGAAAGCTATATGGCTGAGGAATCCAAAAGAGGTTACAGAAGAAGAATACACCAAATTCTACCACTCTCTTGCCAAGgtaa----cat-tgccaatttg-ccatgcttgttccttatacatcaagggaatttattgtgaaattcacttcactgagtttgttaatattcataaagttgtggatttatgttttgtgcag
upper sequence: AT4G24190.2 (Arabidopsis thaliana), 5'ss of exon 9
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 5'ss of exon 9
TGAATGGGAGCTTCTGAATGATGTTAAGGCTATATGGCTGAGAAGTCCAAAGGAGGTGACAGAGGAAGAGTACACTAAATTCTACCACTCTCTCTCAAAGgtgaaaacca--tgcgttaactaaatcatacttgttacatactaggtgtaaaattttcgtgt----ggatttccctgaccccagttgttatacag----------------------
||| ||||||||| |||||||||| |||||||||||| | | | ||||||||||||||| |||||||||||||| ||||||||||| ||||| | |||| || ||| | | || | || | | || | ||||| | | |||| | | | || || ||| ||| | |
TGAGTGGGAGCTTTTGAATGATGTGAAGGCTATATGGTTACGGAATCCAAAGGAGGTGACGGAGGAAGAGTACACAAAATTCTACCAGTCTCTAGCTAAGgcaaattccaattcccttggtttcattacattt-caaaatactctgattgttttttttggcttcccaagtatcactctttccatcagttggataacatattttatcttgttcaacagMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|124904062|gb|EH978142.1|EH978142EST: AGGAGGTGACAGAGGAAGAGTACACTAAATTCTACCACTCTCTCTCAAAG GATTTTACCGACGAGAAGCCAATGGCTTGGAGTCACTTTAATGCTGAAGGT
genomic: AGGAGGTGACAGAGGAAGAGTACACTAAATTCTACCACTCTCTCTCAAAGgtgaaaacca ... tgttatacagGATTTTACCGACGAGAAGCCAATGGCTTGGAGTCACTTTAATGCTGAAGGT
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TGAATGGGAGCTTCTGAATGATGTTAAGGCTATATGGCTGAGAAGTCCAAAGGAGGTGACAGAGGAAGAGTACACTAAATTCTACCACTCTCTCTCAAAGgtgaaaaccatgcgttaactaaatcatacttgttacatactaggtgtaaaattttcgtgtggatttccctgaccccagttgttatacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA